hubward package

Submodules

hubward.generate_config_from_schema module

hubward.generate_config_from_schema.access(dct, keys)

Access a value from an arbitrarily-nested dictionary, given a set of keys.

If any key doesn’t exist, returns None.

>>> access({'a': {'aa': {'aaa': {'b': 1, 'c': 2}}}}, keys=['a', 'aa', 'aaa', 'b'])
1

hubward.generate_config_from_schema.create_config(schema, fout=None)

Generates an example config file based on the schema alone and writes it to fout, which can then be validated.

The goal is to have the schema be the sole source of config files.

“description” fields in the schema will be printed out as YAML comments, serving as documentation.

Parameters:

schema : str

Filename of schema

fout : file-like

Output file to write YAML to.

hubward.generate_config_from_schema.follow_ref(ref, dct)

Follow a “$ref” JSON Schema reference

hubward.generate_config_from_schema.ordered_load(stream, Loader=<class 'yaml.loader.Loader'>, object_pairs_hook=<class 'collections.OrderedDict'>)

Load YAML into an ordered dictionary to maintain key sorting.

hubward.generate_config_from_schema.represent_odict(dump, tag, mapping, flow_style=None)

Dump an ordered dictionary to YAML, maintaining the key order but making it look like a normal dictionary (without the !!python/object extra stuff).

From https://gist.github.com/miracle2k/3184458

hubward.liftover module

Module for converting genomic coordinates from one version of an assembly to another

hubward.liftover.chainfile_url(source_assembly, target_assembly)

hubward.liftover.download_chainfile(source_assembly, target_assembly)

Download if needed, putting in the cache_dir.

If the environmental variable HUBWARD_CACHE_DIR does not exist, then use ~/.hubward_cache

hubward.liftover.liftover(from_, to_, infile, outfile, filetype)

hubward.log module

hubward.log.log(msg, indent=0, style=None)

Generic module-level logging.

Parameters:

msg : string

indent : int

How much to indent the message. Timestamp will remain left-justified.

style : a colorama style

For example, use sytle=colorama.Fore.BLUE for blue text.

hubward.models module

class hubward.models.Data(obj, reldir)

Bases: object

Methods

liftover(from_assembly, to_assembly, newfile)	Lifts over the processed file to a new file, but only if needed.
process()	Run the conversion script if the output needs updating.

liftover(from_assembly, to_assembly, newfile)

Lifts over the processed file to a new file, but only if needed.

Uses a hidden sentinel file to indicate whether it’s been lifted over.

Parameters:

from_assembly : str

Existing data are in this assembly’s coordinates

to_assembly : str

Lift over existing data to this assembly’s coordinates

newfile : str

Target filename of the lifted-over data

process()

Run the conversion script if the output needs updating.

class hubward.models.Group(fn)

Bases: object

Methods

process()
upload([hub_only, host, user, ...])

process()

upload(hub_only=False, host=None, user=None, rsync_options=None, hub_remote=None)

class hubward.models.Study(dirname)

Bases: object

Methods

composite_track()	Create a composite track ready to be added to a trackhub.TrackDb instance.
process([force])
reference_section()	Creates a ReST-formatted reference section to be appended to the end of the documentation for the composite track config page.

composite_track()

Create a composite track ready to be added to a trackhub.TrackDb instance.

process(force=False)

reference_section()

Creates a ReST-formatted reference section to be appended to the end of the documentation for the composite track config page.

If no configured reference or PMID, then return an empty string.

hubward.utils module

hubward.utils.add_chr(f)

Prepend “chr” to the beginning of chromosome names.

Useful when passed to pybedtool.BedTool.each().

hubward.utils.bigbed(filename, genome, output, blockSize=256, itemsPerSlot=512, bedtype=None, _as=None, unc=False, tab=False)

Parameters:

:filename:

BED-like file to convert

:genome:

Assembly string (e.g., “mm10” or “hg19”)

:output:

Path to bigBed file to create.

Other args are passed to bedToBigBed. In particular, `bedtype` (which

becomes the “-type=” argument) is automatically handled for you if it is

kept as the default None.

Assumes that a recent version of bedToBigBed from UCSC is on the path.

hubward.utils.bigwig(filename, genome, output, blockSize=256, itemsPerSlot=512, bedtype=None, _as=None, unc=False, tab=False)

Parameters:

:filename:

BEDGRAPH-like file to convert

:genome:

Assembly string (e.g., “mm10” or “hg19”)

:output:

Path to bigWig file to create.

Other args are passed to bedGraphToBigWig.

hubward.utils.chromsizes(assembly)

hubward.utils.colored_bigbed(x, color, genome, target, autosql=None, bedtype=None)

if color is “smart”, then use metaseq’s smart colormap centered on zero.

otherwise, use singlecolormap.

assumes that you have scores in BedTool x; this will zero all scores in the final bigbed

hubward.utils.colortuple(col)

Given a color in any format supported by matplotlib, return a comma-separated string of R,G,B uint8 values.

hubward.utils.download(url, outfile)

hubward.utils.fix_macs_wig(fn, genome, output=None, add_chr=False, to_ignore=None)

wig files created by MACS often are extended outside the chromsome ranges. This function edits an input WIG file to fit within the chromosome boundaries defined by genome.

If add_chr is True, then prefix each chromosome name with “chr”.

Also gets rid of any track lines so the file is ready for conversion to bigWig.

Returns the output filename.

fn : str

Input WIG filename. Can be gzipped, if extension ends in .gz.

genome : str or dict

output : str or None

If None, writes to temp file

to_ignore : list

List of chromosomes to ignore.

hubward.utils.get_resource(fn, as_tempfile=False)

Retrieve an installed resource.

If an installed resource can’t be found, then assume we’re working out of the source directory in which case we can find the file in the ../resources dir.

By default, returns a string. If as_tempfile=True, then write the string to a tempfile and return that new filename. The caller is responsible for deleting the tempfile.

hubward.utils.is_newer(x, y)

hubward.utils.link_is_newer(x, y)

hubward.utils.make_executable(filename)

hubward.utils.makedirs(dirnames)

Recursively create the given directory or directories without reporting errors if they are present.

hubward.utils.reST_to_html(s)

Convert ReST-formatted string s into HTML.

Output is intended for uploading to UCSC configuration pages, so this uses a whitelist approach for HTML tags.

hubward.utils.sanitize(s, strict=False)

If strict, only allow letters and digits – spaces will be stripped.

Otherwise, convert spaces to underscores.

hubward.utils.singlecolormap(color, func=None, n=64)

Creates a linear colormap where color is the top, and func(color) is the bottom.

func should take an RGB tuple as its only input. If func is None, then use a light gray as the min.

n is the number of levels.

hubward.utils.smart_colormap(vmin, vmax, color_high='#b11902', hue_low=0.6)

Creates a “smart” colormap that is centered on zero, and accounts for asymmetrical vmin and vmax by matching saturation/value of high and low colors.

It works by first creating a colormap from white to color_high. Setting this color to the max(abs([vmin, vmax])), it then determines what the color of min(abs([vmin, vmax])) should be on that scale. Then it shifts the color to the new hue hue_low, and finally creates a new colormap with the new hue-shifted as the low, color_high as the max, and centered on zero.

Parameters:

color_high : color

Can be any format supported by matplotlib. Try “#b11902” for a nice red.

hue_low : float in [0, 1]

Try 0.6 for a nice blue

vmin : float

Lowest value in data you’ll be plotting

vmax : float

Highest value in data you’ll be plotting

hubward.utils.unpack(filename, dest)

hubward.version module

Module contents